Merge branch 'master' of github.com:biomage-org/api into refactor-etag

Signed-off-by: Pol Alvarez <[email protected]>
biomage-org · Oct 25, 2023 · da6da7e · da6da7e
2 parents 9c8c774 + ee69a1c
commit da6da7e
Show file tree

Hide file tree

Showing 3 changed files with 2,217 additions and 1,966 deletions.
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -75,7 +75,7 @@ jobs:
           head-branch-regex: "${{ github.head_ref }}"
           lowercase-branch: false
           body-template: ${{  steps.create-unchecked-pr-body.outputs.body }}
-          body-update-action: "replace"
+          body-update-action: 'replace'
 
   test:
     name: Run tests
@@ -84,64 +84,65 @@ jobs:
     env:
       CI: "true"
     steps:
-      - id: setup-node
-        uses: actions/setup-node@v2
-        with:
-          node-version: "14"
-
-      - id: checkout
-        name: Check out source code
-        uses: actions/checkout@v3
-        with:
-          ref: ${{github.head_ref}}
-          repository: ${{github.event.pull_request.head.repo.full_name}}
-
-      - id: cache-seek
-        name: Check for npm cache hit
-        uses: c-hive/gha-npm-cache@v1
-
-      - id: install
-        name: Install dependencies
-        run: |-
-          echo "Running CI with "
-          echo "Node version: $(node --version)"
-          echo "NPM version: $(npm --version)"
-
-          git config --global url."https://".insteadOf ssh://
-          npm ci
-
-      - id: test-codecov
-        name: Run unit tests with coverage
-        uses: mattallty/jest-github-action@v1
-        env:
-          AWS_DEFAULT_REGION: ${{ secrets.AWS_REGION }}
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-          test-command: "npm run coverage"
-          coverage-comment: false
-
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v1
 
-      - id: check-licenses
-        name: Check licenses
-        env:
-          ALLOWED_LICENSES: "MIT;ISC;Apache-2.0;BSD-3-Clause;BSD-2-Clause;(MIT OR Apache-2.0);Unlicense;Python-2.0;BSD;(AFL-2.1 OR BSD-3-Clause);0BSD"
-          EXCLUDE_PACKAGES: "[email protected]"
-        run: |-
-          npm install -g license-checker
-          license-checker --production --json --onlyAllow="${ALLOWED_LICENSES}" --excludePackages="${EXCLUDE_PACKAGES}"
-
-      - id: send-to-slack
-        name: Send failure notification to Slack
-        if: failure() && github.event_name == 'push'
-        env:
-          SLACK_BOT_TOKEN: ${{ secrets.BUILD_STATUS_BOT_TOKEN }}
-        uses: voxmedia/github-action-slack-notify-build@v1
-        with:
-          channel: pipelines
-          status: FAILED
-          color: danger
+    - id: setup-node
+      uses: actions/setup-node@v2
+      with:
+        node-version: '14'
+
+    - id: checkout
+      name: Check out source code
+      uses: actions/checkout@v3
+      with:
+        ref: ${{github.head_ref}}
+        repository: ${{github.event.pull_request.head.repo.full_name}}
+
+    - id: cache-seek
+      name: Check for npm cache hit
+      uses: c-hive/gha-npm-cache@v1
+
+    - id: install
+      name: Install dependencies
+      run: |-
+        echo "Running CI with "
+        echo "Node version: $(node --version)"
+        echo "NPM version: $(npm --version)"
+
+        git config --global url."https://".insteadOf ssh://
+        npm ci
+
+    - id: test-codecov
+      name: Run unit tests with coverage
+      uses: mattallty/jest-github-action@v1
+      env:
+        AWS_DEFAULT_REGION: ${{ secrets.AWS_REGION }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      with:
+        test-command: "npm run coverage"
+        coverage-comment: false
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v1
+
+    - id: check-licenses
+      name: Check licenses
+      env:
+        ALLOWED_LICENSES: "MIT;ISC;Apache-2.0;BSD-3-Clause;BSD-2-Clause;(MIT OR Apache-2.0);Unlicense;Python-2.0;BSD;(AFL-2.1 OR BSD-3-Clause);0BSD"
+        EXCLUDE_PACKAGES: "[email protected]"
+      run: |-
+        npm install -g license-checker
+        license-checker --production --json --onlyAllow="${ALLOWED_LICENSES}" --excludePackages="${EXCLUDE_PACKAGES}"
+
+    - id: send-to-slack
+      name: Send failure notification to Slack
+      if: failure() && github.event_name == 'push'
+      env:
+        SLACK_BOT_TOKEN: ${{ secrets.BUILD_STATUS_BOT_TOKEN }}
+      uses: voxmedia/github-action-slack-notify-build@v1
+      with:
+        channel: pipelines
+        status: FAILED
+        color: danger
 
   build-docker:
     name: Build Docker container
@@ -261,7 +262,7 @@ jobs:
     strategy:
       max-parallel: 1
       matrix:
-        environment: ["production", "staging", "develop"]
+        environment: ['production', 'staging', 'develop']
     steps:
       - id: checkout
         name: Check out source code
@@ -384,41 +385,43 @@ jobs:
           REF_ID: ${{ needs.build-docker.outputs.ref-id }}
           IMAGE_TAG: ${{ needs.build-docker.outputs.image-tag }}
           REGISTRY: ${{ steps.login-ecr.outputs.registry }}
-
       - name: Push production/develop template to releases
-        if: (matrix.environment == 'production' && github.event_name == 'release' && github.event.action == 'released') || (matrix.environment == 'develop' && github.event_name == 'push')
+        if:
+          (matrix.environment == 'production' && github.event_name == 'release' && github.event.action == 'released') || (matrix.environment == 'develop' && github.event_name == 'push')
         uses: dmnemec/[email protected]
         env:
           API_TOKEN_GITHUB: ${{ secrets.API_TOKEN_GITHUB }}
         with:
-          source_file: "${{ steps.fill-metadata.outputs.deployment-name }}.yaml"
-          destination_repo: "${{ github.repository_owner }}/releases"
-          destination_folder: "${{ steps.fill-metadata.outputs.kubernetes-env }}"
-          user_email: "[email protected]"
-          user_name: "Biomage CI/CD"
+          source_file: '${{ steps.fill-metadata.outputs.deployment-name }}.yaml'
+          destination_repo: '${{ github.repository_owner }}/releases'
+          destination_folder: '${{ steps.fill-metadata.outputs.kubernetes-env }}'
+          user_email: '[email protected]'
+          user_name: 'Biomage CI/CD'
 
       - name: Change name of deployment file for staging deployment
-        if: (github.event_name == 'pull_request_target' || github.event_name == 'push') && matrix.environment == 'staging'
+        if:
+          (github.event_name == 'pull_request_target' || github.event_name == 'push') && matrix.environment == 'staging'
         env:
           DEPLOYMENT_NAME: ${{ steps.fill-metadata.outputs.deployment-name }}
           REF_ID: ${{ needs.build-docker.outputs.ref-id }}
         run: |-
           mv $DEPLOYMENT_NAME.yaml $REF_ID.yaml
 
       - name: Push staging deployment template to releases
-        if: (github.event_name == 'pull_request_target' || github.event_name == 'push') && matrix.environment == 'staging'
+        if:
+          (github.event_name == 'pull_request_target' || github.event_name == 'push') && matrix.environment == 'staging'
         uses: dmnemec/[email protected]
         env:
           API_TOKEN_GITHUB: ${{ secrets.API_TOKEN_GITHUB }}
         with:
           source_file: ${{ needs.build-docker.outputs.ref-id }}.yaml
-          destination_repo: "${{ github.repository_owner }}/releases"
-          destination_folder: "staging-candidates/${{ steps.fill-metadata.outputs.deployment-name }}"
-          user_email: "[email protected]"
-          user_name: "Biomage CI/CD"
-
+          destination_repo: '${{ github.repository_owner }}/releases'
+          destination_folder: 'staging-candidates/${{ steps.fill-metadata.outputs.deployment-name }}'
+          user_email: '[email protected]'
+          user_name: 'Biomage CI/CD'
       - id: disable-admin-enforcement
-        if: (matrix.environment == 'production' && github.event_name == 'release' && github.event.action == 'released') || (matrix.environment == 'develop' && github.event_name == 'push')
+        if:
+          (matrix.environment == 'production' && github.event_name == 'release' && github.event.action == 'released') || (matrix.environment == 'develop' && github.event_name == 'push')
         name: Temporarily disable admin enforcement
         uses: benjefferies/branch-protection-bot@master
         with:
@@ -427,19 +430,19 @@ jobs:
           repo: iac
           enforce_admins: false
           retries: 8
-
       - name: Push migrations into iac
-        if: github.repository_owner == 'hms-dbmi-cellenics' && github.event_name == 'push'
+        if:
+           github.repository_owner == 'hms-dbmi-cellenics' && matrix.environment == 'develop' && github.event_name == 'push'
         uses: cpina/github-action-push-to-another-repository@main
         env:
           API_TOKEN_GITHUB: ${{ secrets.API_TOKEN_GITHUB }}
         with:
-          source-directory: "src/sql/migrations"
-          destination-github-username: "${{ github.repository_owner }}"
-          destination-repository-name: "iac"
-          user-email: "[email protected]"
+          source-directory: 'src/sql/migrations'
+          destination-github-username: '${{ github.repository_owner }}'
+          destination-repository-name: 'iac'
+          user-email: '[email protected]'
           target-branch: master
-          target-directory: "migrations/sql"
+          target-directory: 'migrations/sql'
 
   ready-to-merge:
     name: Ready for merging